Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without... Show moreChlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a bchQ mutant of Chlorobaculum tepidum. The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl c, compared to the wild type (WT). Nearly complete 13C chemical shift assignments were obtained from well-resolved homonuclear 13C-13C RFDR data. For proton assignments heteronuclear 13C-1H (hCH) data sets were collected at 1.2 GHz spinning at 60 kHz. The CHHC experiments revealed intermolecular correlations between 132/31, 132/32, and 121/31, with distance constraints of less than 5 Å. These constraints indicate the syn-anti parallel stacking motif for the aggregates. Fourier transform cryo-EM data reveal an axial repeat of 1.49 nm for the helical tubular aggregates, perpendicular to the inter-tube separation of 2.1 nm. This axial repeat is different from WT and is in line with BChl syn-anti stacks running essentially parallel to the tube axis. Such a packing mode is in agreement with the signature of the Qy band in circular dichroism (CD). Combining the experimental data with computational insight suggests that the packing for the light-harvesting function is similar between WT and bchQ, while the chirality within the chlorosomes is modestly but detectably affected by the reduced compositional heterogeneity in bchQ. Show less
Kamer, J.; Schleier, D.; Donker, M.; Hemberger, P.; Bodi, A.; Bouwman, J. 2023
Correction for 'Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells' by Jelena Belić et al., Phys. Chem. Chem. Phys., 2022, 24, 197-210, https://doi.org... Show moreCorrection for 'Automated assessment of redox potentials for dyes in dye-sensitized photoelectrochemical cells' by Jelena Belić et al., Phys. Chem. Chem. Phys., 2022, 24, 197-210, https://doi.org/10.1039/D1CP04218A. Show less
We have studied the adsorption of O-2 on Cu(111) using supersonic molecular beam techniques. For incident energies ranging between 100 and 400 meV, we have determined the sticking probability as a... Show moreWe have studied the adsorption of O-2 on Cu(111) using supersonic molecular beam techniques. For incident energies ranging between 100 and 400 meV, we have determined the sticking probability as a function of angle of incidence, surface temperature, and coverage. Initial sticking probabilities range from near 0 to 0.85 with an onset near 100 meV, making Cu(111) considerably less reactive than Cu(110) and Cu(100). Normal energy scaling applies and reactivity increases appreciably over the entire range of surface temperatures from 90 to 670 K. A strictly linearly decreasing coverage dependence on sticking precludes adsorption and dissociation via an extrinsic or long-lived mobile precursor state. We cannot exclude that sticking also occurs molecularly at the lowest surface temperatures. However, all tell tales from our experiments suggest that sticking is predominantly direct and dissociative. Comparison to earlier data shows implications for the relative reactivity of Cu(111) vs. Cu/Ru(0001) overlayers. Show less
Borg, G. van der; Crone, N.S.A.; Boyle, A.L.; Kros, A.; Roos, W.H. 2023
Membrane fusion is an essential part of the proper functioning of life. As such it is not only important that organisms carefully regulate the process, but also that it is well understood. One way... Show moreMembrane fusion is an essential part of the proper functioning of life. As such it is not only important that organisms carefully regulate the process, but also that it is well understood. One way to facilitate and study membrane fusion is to use artificial, minimalist, fusion peptides. In this study the efficiency and kinetics of two fusion peptides, denoted CPE and CPK, were studied using single-particle TIRF microscopy. CPE and CPK are helical peptides which interact with each other, forming a coiled-coil motif. The peptides can be inserted into a lipid membrane using a lipid anchor, and if these peptides are anchored in opposing lipid membranes, then the coiled-coil interaction can provide the mechanical force necessary to overcome the energy barrier to initiate fusion, much in the same way the SNARE complex does. In this study we find that the fusogenic facilitation of CPE and CPK in liposomes is, at least partially, dependent on the size of the particle. In addition, under certain fusogenic conditions such as when using small liposomes of similar to 60 nm in diameter, CPK alone is enough to facilitate membrane fusion in both bulk and single-particle studies. We show this using bulk lipid mixing assays utilizing FRET and single-particle TIRF, making use of dequenching fluorophores to indicate fusion. This provides us with new insights into the mechanisms of peptide-mediated membrane fusion and illuminates both challenges as well as opportunities when designing drug delivery systems. Show less
Liu, X.; Cecilio de Oliveira Monteiro, M.; Koper, M.T.M. 2023
Insights into how to control the activity and selectivity of the electrochemical CO2 reduction reaction are still limited because of insufficient knowledge of the reaction mechanism and kinetics,... Show moreInsights into how to control the activity and selectivity of the electrochemical CO2 reduction reaction are still limited because of insufficient knowledge of the reaction mechanism and kinetics, which is partially due to the lack of information on the interfacial pH, an important parameter for proton-coupled reactions like CO2 reduction. Here, we used a reliable and sensitive pH sensor combined with the rotating ring-disk electrode technique, in which a functionalized Au ring electrode works as a real-time detector of the OH- generated during the CO2 reduction reaction at a gold disk electrode. Variations of the interfacial pH due to both electrochemical and homogeneous reactions are mapped and the correlation of the interfacial pH with these reactions is inferred. The interfacial pH near the disk electrode increases from 7 to 12 with increasing current density, with a sharp increase at around -0.5 V vs. RHE, which indicates a change of the dominant buffering species. Through scan rate-dependent voltammetry and chronopotentiometry experiments, the homogenous reactions are shown to reach equilibrium within the time scale of the pH measurements, so that the interfacial concentrations of different carbonaceous species can be calculated using equilibrium constants. Furthermore, pH measurements were also performed under different conditions to disentangle the relationship between the interfacial pH and other electrolyte effects. The buffer effect of alkali metal cations is confirmed, showing that weakly hydrated cations lead to less pronounced pH gradients. Finally, we probe to which extent increasing mass transport and the electrolyte buffer capacity can aid in suppressing the increase of the interfacial pH, showing that the buffer capacity is the dominant factor in suppressing interfacial pH variations. Show less
Hanselman, S.R.; Koper, M.T.M.; Calle Vallejo, F. 2023
Solvent-adsorbate interactions have a great impact on catalytic processes in aqueous systems. Implicit solvent calculations are inexpensive but inaccurate toward hydrogen bonds, while a full... Show moreSolvent-adsorbate interactions have a great impact on catalytic processes in aqueous systems. Implicit solvent calculations are inexpensive but inaccurate toward hydrogen bonds, while a full incorporation of explicit solvation is computationally demanding. Micro-solvation attempts to break this dilemma by including only those solvent molecules directly interacting with the solute and any nearby interfaces, thereby providing a compromise between accuracy and computational expenses. Here, we show that micro-solvation of *OH and its relation to adsorption sites is largely transferable across late transition metal nanoparticles. Solvation energies for *OH on nanoparticles of Ir, Pd, and Pt range from -0.63 +/- 0.04 eV to -0.67 +/- 0.12 eV, while those on Au and Ag are -0.75 +/- 0.07 eV and -1.01 +/- 0.05 eV, respectively. These results enable the use of average solvation corrections for *OH on late transition metal nanostructures. Show less
Willigen, M.J.E. de; Kurahashi, M.; Juurlink, L.B.F. 2022
Oxygen's interaction with Pt surfaces serves as a model system in the development of an accurate theoretical description of reaction mechanisms that involve multiple precursor states. To benchmark... Show moreOxygen's interaction with Pt surfaces serves as a model system in the development of an accurate theoretical description of reaction mechanisms that involve multiple precursor states. To benchmark the influence of surface structure on the dynamics of this interaction, we report absolute values of the initial sticking probability of O-2 onto Pt(111) and two vicinal surfaces for state-selected and rotationally-aligned O-2 molecules. Sticking probabilities vary significantly for helicoptering and cartwheeling molecules. Our data can be understood if normal energy scaling holds for all molecular orientations relative to the surface. Vicinal surfaces are much more reactive than Pt(111) with little to no dependence on the molecule's alignment and a more complex angular dependence. At low incident energies, sticking probabilities are highest for incidence into step facets. The weak alignment dependence points toward predominant scattering into a physisorbed state preceding chemisorbed states over a wide angular range. Show less
Baumgartner, L.-M.; Erbe, A.; Boyle, A.L.; Rabe, M. 2022
The in situ control of reversible protein adsorption to a surface is a critical step towards biofouling prevention and finds utilisation in bioanalytical applications. In this work, adsorption of... Show moreThe in situ control of reversible protein adsorption to a surface is a critical step towards biofouling prevention and finds utilisation in bioanalytical applications. In this work, adsorption of peptides is controlled by employing the electrode potential induced, reversible change of germanium (100) surface termination between a hydrophobic, hydrogen terminated and a hydrophilic, hydroxyl terminated surface. This simple but effective 'smart' interface is used to direct adsorption of two peptides models, representing the naturally highly abundant structural motifs of amphipathic helices and coiled-coils. Their structural similarity coincides with their opposite overall charge and hence allows the examination of the influence of charge and hydrophobicity on adsorption. Polarized attenuated total reflection infrared (ATR-IR) spectroscopy at controlled electrode potential has been used to follow the adsorption process at physiological pH in deuterated buffer. The delicate balance of hydrophobic and electrostatic peptide/surface interactions leads to two different processes upon switching that are both observed in situ: reversible adsorption and reversible reorientation. Negatively charged peptide adsorption can be fully controlled by switching to the hydrophobic interface, while the same switch causes the positively charged, helical peptide to tilt down. This principle can be used for 'smart' adsorption control of a wider variety of proteins and peptides and hence find application, as e.g. a bioanalytical tool or functional biosensor. Show less
Marcandalli, G.; Cecilio de Oliveira Monteiro, M.; Koper, M.T.M. 2021
Electrolyte buffering species have been shown to act as proton donors in the hydrogen evolution reaction (HER). Analogously, we study here whether these electrolyte species may participate in other... Show moreElectrolyte buffering species have been shown to act as proton donors in the hydrogen evolution reaction (HER). Analogously, we study here whether these electrolyte species may participate in other reactions by investigating CO electrooxidation (COOR) on a gold rotating disk electrode. This model system, characterized by fast kinetics, exhibits a dffusion-limited regime, which helps in the identification of the species dictating the diffusion-limited current. Through a systematic concentration dependence study in a variety of buffers, we show that electrolyte buffering species act as oxygen donor shuttles in COOR, lowering the reaction overpotential. A similar correlation between electrolyte and electrocatalytic activity was observed for COOR on a different electrode material (Pt). Probing the electrode-electrolyte interface by attenuated total reflection infrared spectroscopy (ATR-FTIR) and modelling the surface speciation to include the effect of the solution reactions, we propose that the buffer conjugated base generates the oxygen donor (i.e. OH-) through its acid-base reaction with water. Show less
What is the topology of a protein and what governs protein folding to a specific topology? This is a fundamental question in biology. The protein folding reaction is a critically important cellular... Show moreWhat is the topology of a protein and what governs protein folding to a specific topology? This is a fundamental question in biology. The protein folding reaction is a critically important cellular process, which is failing in many prevalent diseases. Understanding protein folding is also key to the design of new proteins for applications. However, our ability to predict the folding of a protein chain is quite limited and much is still unknown about the topological principles of folding. Current predictors of folding kinetics, including the contact order and size, present a limited predictive power, suggesting that these models are fundamentally incomplete. Here, we use a newly developed mathematical framework to define and extract the topology of a native protein conformation beyond knot theory, and investigate the relationship between native topology and folding kinetics in experimentally characterized proteins. We show that not only the folding rate, but also the mechanistic insight into folding mechanisms can be inferred from topological parameters. We identify basic topological features that speed up or slow down the folding process. The approach enabled the decomposition of protein 3D conformation into topologically independent elementary folding units, called circuits. The number of circuits correlates significantly with the folding rate, offering not only an efficient kinetic predictor, but also a tool for a deeper understanding of theoretical folding models. This study contributes to recent work that reveals the critical relevance of topology to protein folding with a new, contact-based, mathematically rigorous perspective. We show that topology can predict folding kinetics when geometry-based predictors like contact order and size fail. Show less
The concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms... Show moreThe concept of dipolar repulsion has been widely used to explain several phenomena in organic chemistry, including the conformational preferences of carbonyl compounds. This model, in which atoms and bonds are viewed as point charges and dipole moment vectors, respectively, is however oversimplified. To provide a causal model rooted in quantitative molecular orbital theory, we have analyzed the rotational isomerism of haloacetaldehydes OHC-CH2X (X = F, Cl, Br, I), using relativistic density functional theory. We have found that the overall trend in the rotational energy profiles is set by the combined effects of Pauli repulsion (introducing a barrier around gauche that separates minima at syn and anti), orbital interactions (which can pull the anti minimum towards anticlinal to maximize hyperconjugation), and electrostatic interactions. Only for X = F, not for X = Cl-I, electrostatic interactions push the preference from syn to anti. Our bonding analyses show how this trend is related to the compact nature of F versus the more diffuse nature of the heavier halogens. Show less
Here we present the results of a study carried out to investigate the simultaneous sulfidation of Co and Mo oxide nanoparticles on Au(111) as a synthesis strategy to prepare a model catalyst for... Show moreHere we present the results of a study carried out to investigate the simultaneous sulfidation of Co and Mo oxide nanoparticles on Au(111) as a synthesis strategy to prepare a model catalyst for hydrodesulfurization (HDS). We make use of scanning tunneling microscopy and X-ray photoelectron spectroscopy to track the changes in morphology and chemistry during the synthesis of a mixed Mo and Co oxide precursor and the sulfidation thereafter, to the respective sulfides. We investigated the effects of temperature and the duration of sulfidation on the completeness of the sulfidation process. Our study shows that the formation of MoS2 with the CoMoS edge (the desired model catalyst) is not affected by the time or the temperature of sulfidation. However, the yield of the Co-promoted MoS2 slabs is limited by the formation of large clusters due to the spreading of Mo and Co oxide phases upon sulfidation. Complete sulfidation of the mixed oxide precursor to Co-promoted MoS2 can be accelerated by increasing the sulfidation temperature to 730 K due to the thermally activated nature of Mo oxide sulfidation. Thus, we demonstrate that using a mixed Mo and Co oxide precursor as a starting point for the Co-promoted MoS2 phase for fundamental catalytic studies is a viable strategy. Show less
